Proteome Remodeling in Response to Sulfur Limitation in “
            <i>Candidatus</i>
            Pelagibacter ubique”

Smith, Daniel P.; Nicora, Carrie; Carini, Paul; Lipton, Mary; Norbeck, Angela D.; Smith, Richard; Giovannoni, Stephen J.

doi:10.1128/msystems.00068-16

Cited by 22 publications

(24 citation statements)

References 90 publications

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“…Best hits for each metagenomic sequence were kept if the alignment length was >90% of the median length of all metagenomic sequences for a given sample. Metagenomic recruitment was expressed in read density per genome using ggplot2 geom_density () and reads per kilobase of genome per million mapped reads (RPKM) as previously reported [ 28 , 87 ].…”

Section: Methodsmentioning

confidence: 99%

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

et al. 2018

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Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden–Meyerhof–Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to freshwater. For strain LSUCC0530, we propose the provisional nomenclature Candidatus fonsibacter ubiquis.

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Section: Methodsmentioning

confidence: 99%

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

et al. 2018

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“…A taxonomic breakdown shows that 39% and 59% of aprA and aprB genes were encoded by Proteobacteria, and only 2% of each gene could be assigned to taxa containing known sulfate reducers (Archaea, Firmicutes, Nitrospirae, and Deltaproteobacteria) (Muyzer and Stams, 2008). These results suggest that the significance of alternative uses for aprA and aprB in oxic waters, namely to detoxify cells by catalyzing the oxidation of sulfite accumulated in the cytoplasm, as described for clades such as SAR11 and SAR116 (Meyer and Kuever, 2007, Smith et al., 2016), may be of global relevance.…”

Section: Resultsmentioning

confidence: 80%

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Salazar

Paoli

Alberti

et al. 2019

Cell

301

363

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SummaryOcean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.Video Abstract

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“…The authors speculated that energy stress may induce chaperone expression as part of a generalized stress response, and that these chaperones are involved in protein protection (Pellitteri-Hahn et al ., 2011). Similarly, the marine chemoorganoheterotroph ‘ Candidatus Pelagibacter ubique’ induced GroEL protein expression under N-starvation (D. P. Smith et al ., 2013), GroES under iron starvation (D. P. Smith et al ., 2010), and the heat shock protein IpbA in nutrient-limited stationary phase (D. P. Smith et al ., 2016). These finding suggest that one role of molecular chaperones during nutrient stress may be to protect key enzymes from proteolytic turnover when cells scavenge peptides to support nutrient-limited sustenance.…”

Section: Resultsmentioning

confidence: 99%